Analyzing lignin biosynthesis pathways in rattan using improved co-expression networks of NACs and MYBs

Abstract

Background: The rattan is a valuable plant resource with multiple applications in tropical forests. Calamus simplicifolius and Daemonorops jenkinsiana are the two most representative rattan species, supplying over 95% of the raw materials for the rattan industry. Hence, the wood properties of both rattans have always attracted researchers' attention.

Results: We re-annotated the genomes, obtained 81 RNA-Seq datasets, and developed an improved pipeline to increase the reliability of co-expression networks of both rattans. Based on the data and pipeline, co-expression relationships were detected in 11 NACs, 49 MYBs, and 86 lignin biosynthesis genes in C. simplicifolius and four NACs, 59 MYBs, and 76 lignin biosynthesis genes in D. jenkinsiana, respectively. Among these co-expression pairs, several genes had a close relationship to the development of wood properties. Additionally, we detected the enzyme gene on the lignin biosynthesis pathway was regulated by either NAC or MYB, while LACCASES was regulated by both NAC and MYB. For D. jenkinsiana, the lignin biosynthesis regulatory network was characterized by positive regulation, and MYB possible negatively regulate non-expressed lignin biosynthesis genes in stem tissues. For C. simplicifolius, NAC may positively regulate highly expressed genes and negatively regulate non-expressed lignin biosynthesis genes in stem tissues. Furthermore, we established core regulatory networks of NAC and MYB for both rattans.

Conclusions: This work improved the accuracy of rattan gene annotation by integrating an efficient co-expression network analysis pipeline, enhancing gene coverage and accuracy of the constructed network, and facilitating an understanding of co-expression relationships among NAC, MYB, and lignin biosynthesis genes in rattan and other plants.

Keywords: Calamus simplicifolius; Daemonorops jenkinsiana; Gene co-expression network; Lignin biosynthesis pathway; NAC and MYB genes.

Fig. 1

Evaluation of gene annotation of C. simplicifolius and D. jenkinsiana. a Number of genes obtained by three gene prediction methods b Alignment of transcriptome data with different annotations. c Comparison of annotations of gene functions (the top is C. simplicifolius and the bottom is D. jenkinsiana)

Fig. 2

Construction and evaluation of the rattan co-expression network. a Distribution of rattan PCC values. b Threshold screening of PCC and MR constructed networks by ROC curve evaluation. c The candidate gene pairs obtained by both methods were evaluated using the ROC curve. (The top is C. simplicifolius and the bottom is D. jenkinsiana) d The summary of co-expression networks in rattan

Fig. 3

Assessing co-expression network reliability using the LHC gene family. a GO enrichment of co-expressed genes in LHC of rattan. (The left is C. simplicifolius, and the right is D. jenkinsiana) b Co-expression link between the LHCAs and LHCBs of rattan. The dark nodes indicate LHCA genes, light nodes indicate rattan’s LHCB genes, orange lines indicate positive regulatory relationships between co-expressed gene pairs, and blue lines indicate negative regulatory relationships between co-expressed gene pairs. c Comparison of PCC top 300 co-expression genes in rattan and Arabidopsis LHCA1. The dark green node indicates D. jenkinsiana. The light green node indicates C. simplicifolius. The yellow node indicates Arabidopsis thaliana. The orange node indicates the LHCA1 gene of each species, the red line indicates the co-expression relationship, and the grey line shows the direct homologous relationship

Fig. 4

Chromosomal mapping of rattan NACs and MYBs. a C. simplicifolius. b D. jenkinsiana

Fig. 5

Heatmap and cluster analysis of the expression of NACs and MYBs in rattan. a and b The heatmap of gene expression in C. simplicifolius. and D. jenkinsiana. c and d. Gene expression pattern clustering map in C. simplicifolius and D. jenkinsiana

Fig. 6

Co-expression genes of NAC and MYB were involved in the lignin biosynthesis pathway. a C. simplicifolius. b D. jenkinsiana

Fig. 7

An overview of the co-expression of NACs and MYBs in the lignin biosynthesis pathway

Fig. 8

Rattan co-expression and regulatory network for NAC and MYB. a and b Regulatory network of NAC, MYB and lignin synthesis-related genes in C. simplicifolius and D. jenkinsiana. c.and d. NAC and MYB core regulatory network in C. simplicifolius and D. jenkinsiana. Green and orange boxes indicate the co-expressed genes of NAC and MYB involved in lignin biosynthesis versus those not involved